DNA microarrays are two-dimensional arrays of reference DNA on glass membranes, microscope slides, or similar substrates. Microarrays are fabricated by spotting small volumes of solution containing reference (probe) DNA onto the substrate. In gene expression profiling assays, cDNA molecules originating from test and control samples competitively bind to the spotted probe molecules on a DNA microarray. The test and the control samples are labeled with two different fluorescent dyes to determine the intensity ratio with a fluorescence scanner. A ratio of one indicates the same expression level and a ratio different from one represents an up- or down-regulation of a respective gene. DNA microarrays can have surfaces covered by thousands of spots, and each spot can contain billions of cDNA probes corresponding to a particular known gene. The targets are poured onto the probe array, the targets hybridize with the complementary probes (if present in the array), and the array is washed to removed target that did not hybridize. This approach allows a parallel, semi-quantitative analysis of thousands of transcription levels in a single experiment. Although the discussion herein uses DNA microarrays as an example, microarrays may also be used for other types of affinity assays than DNA, for example, immunological assays, that rely on the hybridization of biological molecules.
Microarray substrates are often conventional microscope slides with dimensions of 75 by 25 mm. Up to several thousand spots of oligonucleotides or cDNA proves with known identity cover the slide in a two dimensional grid. In a standard experimental set up, a buffered solution containing potential targets is sandwiched between a DNA microarray and a cover slip to form a reaction chamber with an area of several square centimeters and a height of only twenty to a hundred microns. The microarray assembly can be sealed in a humid chamber or placed in a water bath to prevent drying and/or control reaction temperature, and allowed to hybridize for a period of several hours. In such a configuration, diffusion is the only mechanism for DNA strands, or other targets, to move within the reaction chamber. However, diffusion is a notoriously slow process for molecules the size of DNA strands which may need to travel a distance of several centimeters to reach a microarray spot with a complementary probe. In such a case, the immediate vicinity of a probe spot can be quickly depleted, especially in the case of cDNA molecules representing genes with low expression.
This diffusion limitation can lead to low signal-to-noise ratios when a microarray is read because only a fraction of the molecules present in the sample may get a chance to bind to their complimentary spots. Generally speaking, when a microarray's area reaches approximately 22 cm by 22 cm, it can be defined as a large area microarray. For large area microarrays, such as genome-wide DNA microarrays, the diffusion limitation and low signal-to-noise ratios are further exacerbated because of the longer travel distances for the target molecules.
A solution to overcome the diffusion limitation and improve the reaction kinetics for better intensity and uniformity of hybridization is to agitate the target sample solution. The low height and large area of the reaction chamber formed by the microarray and the cover slip can make effective agitation difficult, especially for large area microarrays. Current approaches for agitation of the target sample solution include, for example: (i) microfluidic circulation, (ii) ultrasonic agitation, and (iii) contact with overlayed expanding and contracting air bladders. A drawback of microfluidic circulation is the requirement of three to five times as much target sample solution. The drawbacks of the ultrasonic and air bladder methods include cost and complexity of use, as well as the need for additional consumable materials. Advalytix AG of Brunnthal, Germany markets a line of products based on ultrasonic techniques. BioMicro Systems, Inc. of Salt Lake City, Utah, markets a line of products based on air bladder techniques. Both the ultrasonic and the air bladder techniques are difficult to scale up to handle large area microarrays.
In view of the above discussion, it is very desirable to have a reaction apparatus for use with microarrays that is low cost, easy to use, and capable of effectively agitating large area microarrays.